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Multiplexed enrichment and genomic profiling of peripheral immune cell subsets on a microfluidic chip

Miguel Reyes, Dwayne Vickers, Kianna Billman, Thomas Eisenhaure, Paul Hoover, Edward Browne, Deepak A. Rao, Nir Hacohen, Paul C. Blainey
doi: https://doi.org/10.1101/261321
Miguel Reyes
1Broad Institute of MIT and Harvard, Cambridge, MA, USA.
2Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
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Dwayne Vickers
1Broad Institute of MIT and Harvard, Cambridge, MA, USA.
2Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
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Kianna Billman
1Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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Thomas Eisenhaure
1Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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Paul Hoover
1Broad Institute of MIT and Harvard, Cambridge, MA, USA.
3Division of Rheumatology, Immunology, Allergy, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA.
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Edward Browne
1Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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Deepak A. Rao
3Division of Rheumatology, Immunology, Allergy, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA.
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Nir Hacohen
1Broad Institute of MIT and Harvard, Cambridge, MA, USA.
4Center for Cancer Research, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
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  • For correspondence: nhacohen@broadinstitute.org pblainey@broadinstitute.org
Paul C. Blainey
1Broad Institute of MIT and Harvard, Cambridge, MA, USA.
2Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
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  • For correspondence: nhacohen@broadinstitute.org pblainey@broadinstitute.org
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ABSTRACT

The human immune system consists of many specialized cell subsets that simultaneously carry out a diverse range of functions using overlapping pathways and signals. Subset-specific immune profiling can resolve immune activity in autoimmune disease, cancer immunity, and infectious disease that may not be discoverable or detectable in analyses of crude blood samples. The activity of specific subsets may help predict the course of disease and response to therapy in certain patient populations. Here, we present a low-input microfluidic system for sorting immune cells into subsets and profiling their cellular states by gene expression analysis using full-length RNA-seq. Our system is robust and has the potential to make multiplexed subset-specific analysis routine in many research laboratories and clinical settings. We validate the device’s technical performance by benchmarking its subset enrichment and genomic profiling performance against standard protocols. We make the added value of subset-resolved profiling over crude samples clear through ex vivo experiments that show subset-specific stimulated responses. Finally, we demonstrate the scalability of our device by profiling four immune cell subsets in blood from systemic lupus erythematosus (SLE) patients and matched controls enrolled in a clinical study. The results from our initial cohort confirm the role of type I interferons in lupus pathogenesis and further show that the canonical interferon signature for SLE is prominent in B cells, demonstrating the ability of our integrated analytical platform to identify cell-specific disease signatures.

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Posted February 07, 2018.
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Multiplexed enrichment and genomic profiling of peripheral immune cell subsets on a microfluidic chip
Miguel Reyes, Dwayne Vickers, Kianna Billman, Thomas Eisenhaure, Paul Hoover, Edward Browne, Deepak A. Rao, Nir Hacohen, Paul C. Blainey
bioRxiv 261321; doi: https://doi.org/10.1101/261321
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Multiplexed enrichment and genomic profiling of peripheral immune cell subsets on a microfluidic chip
Miguel Reyes, Dwayne Vickers, Kianna Billman, Thomas Eisenhaure, Paul Hoover, Edward Browne, Deepak A. Rao, Nir Hacohen, Paul C. Blainey
bioRxiv 261321; doi: https://doi.org/10.1101/261321

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